Tempo and Mode of Genome Evolution in the Budding Yeast Subphylum

Autores: Shen, Xing-Xing; Opulente, Dana A.; Kominek, Jacek; Zhou, Xiaofan; Steenwyk, Jacob L.; Buh, Kelly V.; Haase, Max A.B.; Wisecaver, Jennifer H.; Wang, Mingshuang; Doering, Drew T.; Boudouris, James T.; Schneider, Rachel M.; Langdon, Quinn K.; Ohkuma, Moriya; Endoh, Rikiya; Takashima, Masako; Manabe, Ri-ichiroh; Čadež, Neža; Libkind Frati, Diego; Rosa, Carlos A.; DeVirgilio, Jeremy; Hulfachor, Amanda Beth; Groenewald, Marizeth; Kurtzman, Cletus P.; Hittinger, Chris Todd; Rokas, Antonis
Año de publicación: 2018
Idioma: inglés
Tipo de recurso: artículo
Estado: versión publicada
Descripción: Budding yeasts (subphylum Saccharomycotina) are found in every biome and are as genetically diverse as plants or animals. To understand budding yeast evolution, we analyzed the genomes of 332 yeast species, including 220 newly sequenced ones, which represent nearly one-third of all known budding yeast diversity. Here, we establish a robust genus-level phylogeny comprising 12 major clades, infer the timescale of diversification from the Devonian period to the present, quantify horizontal gene transfer (HGT), and reconstruct the evolution of 45 metabolic traits and the metabolic toolkit of the budding yeast common ancestor (BYCA). We infer that BYCA was metabolically complex and chronicle the tempo and mode of genomic and phenotypic evolution across the subphylum, which is characterized by very low HGT levels and widespread losses of traits and the genes that control them. More generally, our results argue that reductive evolution is a major mode of evolutionary diversification.
Fil: Shen, Xing-Xing. Vanderbilt University; Estados Unidos
Fil: Opulente, Dana A.. University of Wisconsin; Estados Unidos
Fil: Kominek, Jacek. University of Wisconsin; Estados Unidos
Fil: Zhou, Xiaofan. Vanderbilt University; Estados Unidos. South China Agricultural University; China
Fil: Steenwyk, Jacob L.. Vanderbilt University; Estados Unidos
Fil: Buh, Kelly V.. University of Wisconsin; Estados Unidos
Fil: Haase, Max A.B.. University of Wisconsin; Estados Unidos. University of New York. School of Medicine; Estados Unidos
Fil: Wisecaver, Jennifer H.. Purdue University; Estados Unidos. Vanderbilt University; Estados Unidos
Fil: Wang, Mingshuang. Vanderbilt University; Estados Unidos
Fil: Doering, Drew T.. University of Wisconsin; Estados Unidos
Fil: Boudouris, James T.. University of Wisconsin; Estados Unidos
Fil: Schneider, Rachel M.. University of Wisconsin; Estados Unidos
Fil: Langdon, Quinn K.. University of Wisconsin; Estados Unidos
Fil: Ohkuma, Moriya. Riken BioResource Research Center. Japan Collection of Microorganisms; Japón
Fil: Endoh, Rikiya. Riken BioResource Research Center. Japan Collection of Microorganisms; Japón
Fil: Takashima, Masako. Riken BioResource Research Center. Japan Collection of Microorganisms; Japón
Fil: Manabe, Ri-ichiroh. Riken Center for Integrative Medical Sciences; Japón. Riken Center For Life Science Technologies; Japón
Fil: Čadež, Neža. University of Ljubljana; Eslovenia
Fil: Libkind Frati, Diego. Consejo Nacional de Investigaciones Científicas y Técnicas. Centro Científico Tecnológico Conicet - Patagonia Norte. Instituto Andino Patagónico de Tecnologías Biológicas y Geoambientales. Universidad Nacional del Comahue. Instituto Andino Patagónico de Tecnologías Biológicas y Geoambientales.; Argentina. Universidad Nacional del Comahue. Centro Regional Universitario Bariloche; Argentina
Fil: Rosa, Carlos A.. Universidade Federal de Minas Gerais; Brasil
Fil: DeVirgilio, Jeremy. United States Department of Agriculture. Agricultural Research Service; Argentina. National Center For Agricultural; Estados Unidos
Fil: Hulfachor, Amanda Beth. University of Wisconsin; Estados Unidos
Fil: Groenewald, Marizeth. Westerdijk Fungal Biodiversity Institute; Países Bajos
Fil: Kurtzman, Cletus P.. United States Department of Agriculture. Agricultural Research Service; Argentina. National Center For Agricultural; Estados Unidos
Fil: Hittinger, Chris Todd. University of Wisconsin; Estados Unidos
Fil: Rokas, Antonis. Vanderbilt University; Estados Unidos
Materia: AND REDUCTIVE EVOLUTION
ASCOMYCOTA
GENOMICS
HIGH-THROUGHPUT SEQUENCING
HORIZONTAL GENE TRANSFER
METABOLIC TRAITS
MOLECULAR DATING
PHYLOGENETICS
PHYLOGENOMICS
SACCHAROMYCOTINA
Nivel de accesibilidad: acceso abierto
Condiciones de uso: https://creativecommons.org/licenses/by-nc-sa/2.5/ar/
Repositorio
Institución: Consejo Nacional de Investigaciones Científicas y Técnicas
OAI Identificador: oai:ri.conicet.gov.ar:11336/89318

Acceder

id	CONICETDig_949e1078bd2fdf73d324418eaf97bd17
oai_identifier_str	oai:ri.conicet.gov.ar:11336/89318
network_acronym_str	CONICETDig
repository_id_str	3498
network_name_str	CONICET Digital (CONICET)
spelling	Tempo and Mode of Genome Evolution in the Budding Yeast SubphylumShen, Xing-XingOpulente, Dana A.Kominek, JacekZhou, XiaofanSteenwyk, Jacob L.Buh, Kelly V.Haase, Max A.B.Wisecaver, Jennifer H.Wang, MingshuangDoering, Drew T.Boudouris, James T.Schneider, Rachel M.Langdon, Quinn K.Ohkuma, MoriyaEndoh, RikiyaTakashima, MasakoManabe, Ri-ichirohČadež, NežaLibkind Frati, DiegoRosa, Carlos A.DeVirgilio, JeremyHulfachor, Amanda BethGroenewald, MarizethKurtzman, Cletus P.Hittinger, Chris ToddRokas, AntonisAND REDUCTIVE EVOLUTIONASCOMYCOTAGENOMICSHIGH-THROUGHPUT SEQUENCINGHORIZONTAL GENE TRANSFERMETABOLIC TRAITSMOLECULAR DATINGPHYLOGENETICSPHYLOGENOMICSSACCHAROMYCOTINAhttps://purl.org/becyt/ford/1.6https://purl.org/becyt/ford/1Budding yeasts (subphylum Saccharomycotina) are found in every biome and are as genetically diverse as plants or animals. To understand budding yeast evolution, we analyzed the genomes of 332 yeast species, including 220 newly sequenced ones, which represent nearly one-third of all known budding yeast diversity. Here, we establish a robust genus-level phylogeny comprising 12 major clades, infer the timescale of diversification from the Devonian period to the present, quantify horizontal gene transfer (HGT), and reconstruct the evolution of 45 metabolic traits and the metabolic toolkit of the budding yeast common ancestor (BYCA). We infer that BYCA was metabolically complex and chronicle the tempo and mode of genomic and phenotypic evolution across the subphylum, which is characterized by very low HGT levels and widespread losses of traits and the genes that control them. More generally, our results argue that reductive evolution is a major mode of evolutionary diversification.Fil: Shen, Xing-Xing. Vanderbilt University; Estados UnidosFil: Opulente, Dana A.. University of Wisconsin; Estados UnidosFil: Kominek, Jacek. University of Wisconsin; Estados UnidosFil: Zhou, Xiaofan. Vanderbilt University; Estados Unidos. South China Agricultural University; ChinaFil: Steenwyk, Jacob L.. Vanderbilt University; Estados UnidosFil: Buh, Kelly V.. University of Wisconsin; Estados UnidosFil: Haase, Max A.B.. University of Wisconsin; Estados Unidos. University of New York. School of Medicine; Estados UnidosFil: Wisecaver, Jennifer H.. Purdue University; Estados Unidos. Vanderbilt University; Estados UnidosFil: Wang, Mingshuang. Vanderbilt University; Estados UnidosFil: Doering, Drew T.. University of Wisconsin; Estados UnidosFil: Boudouris, James T.. University of Wisconsin; Estados UnidosFil: Schneider, Rachel M.. University of Wisconsin; Estados UnidosFil: Langdon, Quinn K.. University of Wisconsin; Estados UnidosFil: Ohkuma, Moriya. Riken BioResource Research Center. Japan Collection of Microorganisms; JapónFil: Endoh, Rikiya. Riken BioResource Research Center. Japan Collection of Microorganisms; JapónFil: Takashima, Masako. Riken BioResource Research Center. Japan Collection of Microorganisms; JapónFil: Manabe, Ri-ichiroh. Riken Center for Integrative Medical Sciences; Japón. Riken Center For Life Science Technologies; JapónFil: Čadež, Neža. University of Ljubljana; EsloveniaFil: Libkind Frati, Diego. Consejo Nacional de Investigaciones Científicas y Técnicas. Centro Científico Tecnológico Conicet - Patagonia Norte. Instituto Andino Patagónico de Tecnologías Biológicas y Geoambientales. Universidad Nacional del Comahue. Instituto Andino Patagónico de Tecnologías Biológicas y Geoambientales.; Argentina. Universidad Nacional del Comahue. Centro Regional Universitario Bariloche; ArgentinaFil: Rosa, Carlos A.. Universidade Federal de Minas Gerais; BrasilFil: DeVirgilio, Jeremy. United States Department of Agriculture. Agricultural Research Service; Argentina. National Center For Agricultural; Estados UnidosFil: Hulfachor, Amanda Beth. University of Wisconsin; Estados UnidosFil: Groenewald, Marizeth. Westerdijk Fungal Biodiversity Institute; Países BajosFil: Kurtzman, Cletus P.. United States Department of Agriculture. Agricultural Research Service; Argentina. National Center For Agricultural; Estados UnidosFil: Hittinger, Chris Todd. University of Wisconsin; Estados UnidosFil: Rokas, Antonis. Vanderbilt University; Estados UnidosCell Press2018-11info:eu-repo/semantics/articleinfo:eu-repo/semantics/publishedVersionhttp://purl.org/coar/resource_type/c_6501info:ar-repo/semantics/articuloapplication/pdfapplication/vnd.openxmlformats-officedocument.wordprocessingml.documentapplication/pdfapplication/pdfhttp://hdl.handle.net/11336/89318Shen, Xing-Xing; Opulente, Dana A.; Kominek, Jacek; Zhou, Xiaofan; Steenwyk, Jacob L.; et al.; Tempo and Mode of Genome Evolution in the Budding Yeast Subphylum; Cell Press; Cell; 175; 6; 11-2018; 1533-15450092-8674CONICET DigitalCONICETenginfo:eu-repo/semantics/altIdentifier/url/https://www.sciencedirect.com/science/article/pii/S009286741831332info:eu-repo/semantics/altIdentifier/doi/10.1016/j.cell.2018.10.023info:eu-repo/semantics/openAccesshttps://creativecommons.org/licenses/by-nc-sa/2.5/ar/reponame:CONICET Digital (CONICET)instname:Consejo Nacional de Investigaciones Científicas y Técnicas2025-09-29T10:07:39Zoai:ri.conicet.gov.ar:11336/89318instacron:CONICETInstitucionalhttp://ri.conicet.gov.ar/Organismo científico-tecnológicoNo correspondehttp://ri.conicet.gov.ar/oai/requestdasensio@conicet.gov.ar; lcarlino@conicet.gov.arArgentinaNo correspondeNo correspondeNo correspondeopendoar:34982025-09-29 10:07:40.165CONICET Digital (CONICET) - Consejo Nacional de Investigaciones Científicas y Técnicasfalse
dc.title.none.fl_str_mv	Tempo and Mode of Genome Evolution in the Budding Yeast Subphylum
title	Tempo and Mode of Genome Evolution in the Budding Yeast Subphylum
spellingShingle	Tempo and Mode of Genome Evolution in the Budding Yeast Subphylum Shen, Xing-Xing AND REDUCTIVE EVOLUTION ASCOMYCOTA GENOMICS HIGH-THROUGHPUT SEQUENCING HORIZONTAL GENE TRANSFER METABOLIC TRAITS MOLECULAR DATING PHYLOGENETICS PHYLOGENOMICS SACCHAROMYCOTINA
title_short	Tempo and Mode of Genome Evolution in the Budding Yeast Subphylum
title_full	Tempo and Mode of Genome Evolution in the Budding Yeast Subphylum
title_fullStr	Tempo and Mode of Genome Evolution in the Budding Yeast Subphylum
title_full_unstemmed	Tempo and Mode of Genome Evolution in the Budding Yeast Subphylum
title_sort	Tempo and Mode of Genome Evolution in the Budding Yeast Subphylum
dc.creator.none.fl_str_mv	Shen, Xing-Xing Opulente, Dana A. Kominek, Jacek Zhou, Xiaofan Steenwyk, Jacob L. Buh, Kelly V. Haase, Max A.B. Wisecaver, Jennifer H. Wang, Mingshuang Doering, Drew T. Boudouris, James T. Schneider, Rachel M. Langdon, Quinn K. Ohkuma, Moriya Endoh, Rikiya Takashima, Masako Manabe, Ri-ichiroh Čadež, Neža Libkind Frati, Diego Rosa, Carlos A. DeVirgilio, Jeremy Hulfachor, Amanda Beth Groenewald, Marizeth Kurtzman, Cletus P. Hittinger, Chris Todd Rokas, Antonis
author	Shen, Xing-Xing
author_facet	Shen, Xing-Xing Opulente, Dana A. Kominek, Jacek Zhou, Xiaofan Steenwyk, Jacob L. Buh, Kelly V. Haase, Max A.B. Wisecaver, Jennifer H. Wang, Mingshuang Doering, Drew T. Boudouris, James T. Schneider, Rachel M. Langdon, Quinn K. Ohkuma, Moriya Endoh, Rikiya Takashima, Masako Manabe, Ri-ichiroh Čadež, Neža Libkind Frati, Diego Rosa, Carlos A. DeVirgilio, Jeremy Hulfachor, Amanda Beth Groenewald, Marizeth Kurtzman, Cletus P. Hittinger, Chris Todd Rokas, Antonis
author_role	author
author2	Opulente, Dana A. Kominek, Jacek Zhou, Xiaofan Steenwyk, Jacob L. Buh, Kelly V. Haase, Max A.B. Wisecaver, Jennifer H. Wang, Mingshuang Doering, Drew T. Boudouris, James T. Schneider, Rachel M. Langdon, Quinn K. Ohkuma, Moriya Endoh, Rikiya Takashima, Masako Manabe, Ri-ichiroh Čadež, Neža Libkind Frati, Diego Rosa, Carlos A. DeVirgilio, Jeremy Hulfachor, Amanda Beth Groenewald, Marizeth Kurtzman, Cletus P. Hittinger, Chris Todd Rokas, Antonis
author2_role	author author author author author author author author author author author author author author author author author author author author author author author author author
dc.subject.none.fl_str_mv	AND REDUCTIVE EVOLUTION ASCOMYCOTA GENOMICS HIGH-THROUGHPUT SEQUENCING HORIZONTAL GENE TRANSFER METABOLIC TRAITS MOLECULAR DATING PHYLOGENETICS PHYLOGENOMICS SACCHAROMYCOTINA
topic	AND REDUCTIVE EVOLUTION ASCOMYCOTA GENOMICS HIGH-THROUGHPUT SEQUENCING HORIZONTAL GENE TRANSFER METABOLIC TRAITS MOLECULAR DATING PHYLOGENETICS PHYLOGENOMICS SACCHAROMYCOTINA
purl_subject.fl_str_mv	https://purl.org/becyt/ford/1.6 https://purl.org/becyt/ford/1
dc.description.none.fl_txt_mv	Budding yeasts (subphylum Saccharomycotina) are found in every biome and are as genetically diverse as plants or animals. To understand budding yeast evolution, we analyzed the genomes of 332 yeast species, including 220 newly sequenced ones, which represent nearly one-third of all known budding yeast diversity. Here, we establish a robust genus-level phylogeny comprising 12 major clades, infer the timescale of diversification from the Devonian period to the present, quantify horizontal gene transfer (HGT), and reconstruct the evolution of 45 metabolic traits and the metabolic toolkit of the budding yeast common ancestor (BYCA). We infer that BYCA was metabolically complex and chronicle the tempo and mode of genomic and phenotypic evolution across the subphylum, which is characterized by very low HGT levels and widespread losses of traits and the genes that control them. More generally, our results argue that reductive evolution is a major mode of evolutionary diversification. Fil: Shen, Xing-Xing. Vanderbilt University; Estados Unidos Fil: Opulente, Dana A.. University of Wisconsin; Estados Unidos Fil: Kominek, Jacek. University of Wisconsin; Estados Unidos Fil: Zhou, Xiaofan. Vanderbilt University; Estados Unidos. South China Agricultural University; China Fil: Steenwyk, Jacob L.. Vanderbilt University; Estados Unidos Fil: Buh, Kelly V.. University of Wisconsin; Estados Unidos Fil: Haase, Max A.B.. University of Wisconsin; Estados Unidos. University of New York. School of Medicine; Estados Unidos Fil: Wisecaver, Jennifer H.. Purdue University; Estados Unidos. Vanderbilt University; Estados Unidos Fil: Wang, Mingshuang. Vanderbilt University; Estados Unidos Fil: Doering, Drew T.. University of Wisconsin; Estados Unidos Fil: Boudouris, James T.. University of Wisconsin; Estados Unidos Fil: Schneider, Rachel M.. University of Wisconsin; Estados Unidos Fil: Langdon, Quinn K.. University of Wisconsin; Estados Unidos Fil: Ohkuma, Moriya. Riken BioResource Research Center. Japan Collection of Microorganisms; Japón Fil: Endoh, Rikiya. Riken BioResource Research Center. Japan Collection of Microorganisms; Japón Fil: Takashima, Masako. Riken BioResource Research Center. Japan Collection of Microorganisms; Japón Fil: Manabe, Ri-ichiroh. Riken Center for Integrative Medical Sciences; Japón. Riken Center For Life Science Technologies; Japón Fil: Čadež, Neža. University of Ljubljana; Eslovenia Fil: Libkind Frati, Diego. Consejo Nacional de Investigaciones Científicas y Técnicas. Centro Científico Tecnológico Conicet - Patagonia Norte. Instituto Andino Patagónico de Tecnologías Biológicas y Geoambientales. Universidad Nacional del Comahue. Instituto Andino Patagónico de Tecnologías Biológicas y Geoambientales.; Argentina. Universidad Nacional del Comahue. Centro Regional Universitario Bariloche; Argentina Fil: Rosa, Carlos A.. Universidade Federal de Minas Gerais; Brasil Fil: DeVirgilio, Jeremy. United States Department of Agriculture. Agricultural Research Service; Argentina. National Center For Agricultural; Estados Unidos Fil: Hulfachor, Amanda Beth. University of Wisconsin; Estados Unidos Fil: Groenewald, Marizeth. Westerdijk Fungal Biodiversity Institute; Países Bajos Fil: Kurtzman, Cletus P.. United States Department of Agriculture. Agricultural Research Service; Argentina. National Center For Agricultural; Estados Unidos Fil: Hittinger, Chris Todd. University of Wisconsin; Estados Unidos Fil: Rokas, Antonis. Vanderbilt University; Estados Unidos
description	Budding yeasts (subphylum Saccharomycotina) are found in every biome and are as genetically diverse as plants or animals. To understand budding yeast evolution, we analyzed the genomes of 332 yeast species, including 220 newly sequenced ones, which represent nearly one-third of all known budding yeast diversity. Here, we establish a robust genus-level phylogeny comprising 12 major clades, infer the timescale of diversification from the Devonian period to the present, quantify horizontal gene transfer (HGT), and reconstruct the evolution of 45 metabolic traits and the metabolic toolkit of the budding yeast common ancestor (BYCA). We infer that BYCA was metabolically complex and chronicle the tempo and mode of genomic and phenotypic evolution across the subphylum, which is characterized by very low HGT levels and widespread losses of traits and the genes that control them. More generally, our results argue that reductive evolution is a major mode of evolutionary diversification.
publishDate	2018
dc.date.none.fl_str_mv	2018-11
dc.type.none.fl_str_mv	info:eu-repo/semantics/article info:eu-repo/semantics/publishedVersion http://purl.org/coar/resource_type/c_6501 info:ar-repo/semantics/articulo
format	article
status_str	publishedVersion
dc.identifier.none.fl_str_mv	http://hdl.handle.net/11336/89318 Shen, Xing-Xing; Opulente, Dana A.; Kominek, Jacek; Zhou, Xiaofan; Steenwyk, Jacob L.; et al.; Tempo and Mode of Genome Evolution in the Budding Yeast Subphylum; Cell Press; Cell; 175; 6; 11-2018; 1533-1545 0092-8674 CONICET Digital CONICET
url	http://hdl.handle.net/11336/89318
identifier_str_mv	Shen, Xing-Xing; Opulente, Dana A.; Kominek, Jacek; Zhou, Xiaofan; Steenwyk, Jacob L.; et al.; Tempo and Mode of Genome Evolution in the Budding Yeast Subphylum; Cell Press; Cell; 175; 6; 11-2018; 1533-1545 0092-8674 CONICET Digital CONICET
dc.language.none.fl_str_mv	eng
language	eng
dc.relation.none.fl_str_mv	info:eu-repo/semantics/altIdentifier/url/https://www.sciencedirect.com/science/article/pii/S009286741831332 info:eu-repo/semantics/altIdentifier/doi/10.1016/j.cell.2018.10.023
dc.rights.none.fl_str_mv	info:eu-repo/semantics/openAccess https://creativecommons.org/licenses/by-nc-sa/2.5/ar/
eu_rights_str_mv	openAccess
rights_invalid_str_mv	https://creativecommons.org/licenses/by-nc-sa/2.5/ar/
dc.format.none.fl_str_mv	application/pdf application/vnd.openxmlformats-officedocument.wordprocessingml.document application/pdf application/pdf
dc.publisher.none.fl_str_mv	Cell Press
publisher.none.fl_str_mv	Cell Press
dc.source.none.fl_str_mv	reponame:CONICET Digital (CONICET) instname:Consejo Nacional de Investigaciones Científicas y Técnicas
reponame_str	CONICET Digital (CONICET)
collection	CONICET Digital (CONICET)
instname_str	Consejo Nacional de Investigaciones Científicas y Técnicas
repository.name.fl_str_mv	CONICET Digital (CONICET) - Consejo Nacional de Investigaciones Científicas y Técnicas
repository.mail.fl_str_mv	dasensio@conicet.gov.ar; lcarlino@conicet.gov.ar
_version_	1844613939122405376
score	13.070432

Tempo and Mode of Genome Evolution in the Budding Yeast Subphylum

Publicaciones similares